Just when you think you know what you are doing…

Jennifer AppleJennifer Apple

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Guava flow cytometer

A large part of my research is collecting samples and following protocols to determine dissolved organic carbon (DOC), particulate organic carbon (POC), bacterial abundance and community composition. While the sampling and preparation for analysis can be done at Friday Harbor Labs, the actual analysis requires more specialized equipment than what we have on hand. So this week I traveled to the Seattle campus of University of Washington to drop off my DOC & POC samples to the Marine Chemistry Laboratory. The next stop was Dr. Morris’ lab to check-in with my progress on the project and to learn the protocols for using the ‘Guava’ – the flow cytometer which counts bacterial abundance in our mesocosm samples. The day was spent with new tools and software and was interesting and fun. It was a fantastic experience and one I will get to repeat at the end of the experiment when our sampling is complete.

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Working together in the lab

Then the week started to get interesting. Protocols are established and followed and experiments run smoothly, right? Not so fast! Within a few days of returning to FHL, I found out that my POC sampling was not putting enough mesocosm seawater through the filters causing issues with the accuracy of the analysis. Okay, time to change the protocol and up the amount of water sampled from the mesocosm. Next up, the DOC analysis was completed and the values returned varied widely after the first few days. An evening of research pointed to contamination of the samples. Our amazing technician, Mike Foy, was in the lab and showed me how to acid wash all my sampling equipment. He and I came up with a new protocol to use an acid washed syringe for each mesocosm, acid washed sampling bottles, gloves on the dock and a LOT of Milli-Q to flush the filter screens between samples. Hopefully this will solve the contamination issues.

Science isn’t just about lab work and protocols. The tricky part has been to make sense of all the data points which are coming your way. No matter what software program is used to organize and make sense of your data, there is still time and effort which must be put into entering the data and determining the best method to present it to others. This is where I am grateful to my team. I was completely stumped as to how to get Excel, my preferred program, to create a graph the bacterial abundance trend among the three treatments and comparing them to the dock. Just when I thought I knew what I was doing…I didn’t! Thankfully, my team came to my rescue and showed me how to organize and format my graph. While there are only a few days of data, it is interesting to see differences among the three treatments beginning to develop. See for yourself:

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 I will be most interested to see what the bacterial cell count will be for the remaining days of the experiment. Observation of my filters today showed the High treatment containing much more biomass and coloration than the Control and Drift treatments. While my observations are not scientific, my hypothesis currently is that the High treatment will eventually overtake the Control for the greater number of cells per milliliter. I cannot wait to see what happens next!

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High, Control & Drift filters capturing bacterial DNA

This week has proven again that the best laid plans often go awry. We are learning as a group that sometimes we must change what we are doing to better measure results and that just when you think you know what you are doing you find out you need a little help from your team to reach the finish line.

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